I made after tax contribution to Roth IRA that is separate from my pre-tax 401k. There is a section on turbotax asking for after tax contributions, do I enter Roth $$$?

Where are you in the program ?    Are you entering a 1099-R for the distribution of a retirement account of some kind ?

If the Roth contribution was made under the same employer plan as the 401(k) contribution, it's a contribution to a Roth 401(k), not a to a Roth IRA.  Any amounts reported in box 12 of your W-2 should be entered only in box 12 of TurboTax's W-2 form, nowhere else.

Sorry but now I can't find the section of the program I was in that asked me that question.  I know that it was not on the W-2 Income section.  I do deposit after tax $$$ to Roth IRA but it is NOT the same organization (or investment firm) as my 401k so I am assuming that section asking me about all of this does not apply.

Perhaps it was in the Retirement Savings Contributions Credit section.  No, Roth IRA contributions are not entered in that section.  That section is asking about traditional after-tax contributions to an employer plan, not Roth contributions.

If you truly have a ROTH IRA outside of the payroll system then those contributions are entered in the Deductions & Credits tab under the Retirement section.